The focus of this dissertation is on the regulation of water processing and feeding mechanisms in suspension-feeding bivalve molluscs. In particular it addresses the two currently debated schools of thought regarding the loci of control and biophysics of water processing rates in bivalves. Within these mainly opposing viewpoints, water processing activity is seen either as autonomically regulated, with the ciliary pump functioning at a single, evolutionarily adapted rate, or as physiologically regulated to meet nutritional and metabolic needs. There are many published studies providing excellent support for both positions. The present work attempts to address the arguments presented by both sides, in part by applying new technology to assist in measuring and visualizing volume flux through the animal. Planar (2D) particle image velocimetry (PIV) was used to visualize and calculate flow fields generated by water processing activity in three species of bivalves: blue mussels, Mytilus edulis; Atlantic bay scallops, Argopecten irradians; and eastern oysters, Crassostrea virginica. Four potential loci of control were examined in the studies; exhalant velocity (V), cross-sectional area of the exhalant aperture (Ax), clearance rate (CR) and ctenidial morphology. Volume flux (Q) was calculated as the product of V and Ax. Studies examined modulation of pumping activity either in the presence of a variety of endogenously secreted neuromodulatory agents (e.g., serotonin and phorbol esters), or under conditions of varying diet quality and quantity. Major findings of the studies included the following: 1) effects of neuromodulators on isolated ctenidial tissue were not the same as the effect in vivo; 2) in vivo responses of mussels were different than those of scallops both when exposed to the same neuromodulatory agents and in some cases the same feeding regimes; and 3) control of water processing and feeding can be decoupled and altered independently in both mussels and scallops. The implications of these results are two-fold: 1) points of disagreement are, in part, a matter of differential interpretations of the same data sets, and are, to some degree, semantic; and 2) both autonomous and physiological regulatory mechanisms of control can be employed in species-specific manners.